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Article|01 May 2021|OPEN
The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative
Guillermo Sánchez-de la Vega1, Jonás A. Aguirre-Liguori2, Gabriela Castellanos-Morales3, Yocelyn T. Gutiérrez-Guerrero1, Xitlali Aguirre-Dugua 1, Erika Aguirre-Planter1, Maud I. Tenaillon4, Josué Barrera-Redondo1,, Rafael Lira-Saade5 & Luis E. Eguiarte1,
1Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, México
2Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
3Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Villahermosa, Carretera Villahermosa‐Reforma km 15.5 Ranchería El Guineo 2ª sección, 86280 Villahermosa, Tabasco, México
4Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette 91190, France
5UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios #1, Col. Los Reyes Iztacala, Tlalnepantla, Edo. de Mex 54090, México

Horticulture Research 8,
Article number: 109 (2021)
doi: 10.1038/hortres.2021.109
Views: 183

Received: 09 Nov 2020
Revised: 21 Mar 2021
Accepted: 14 Mar 2021
Published online: 01 May 2021

Abstract

Despite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.